A First-Order System Least-Squares Finite Element Method for the Poisson-Boltzmann Equation
A First-Order System Least-Squares Finite Element Method for the Poisson-Boltzmann Equation
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DOI：
10.1002/jcc.21446
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发表时间：
2010-06-01
影响因子：
3
通讯作者：
Olson, Luke N.
中科院分区：
文献类型：
--
作者：
Bond, Stephen D.;Chaudhry, Jehanzeb Hameed;Olson, Luke N.
Poisson-Boltzmann方程是模拟生物分子体系中溶剂的重要工具。在这篇文章中。我们专注于数值近似的静电势表示在正规化的线性Poisson-Boltzmann方程。我们直接通过方程的一阶系统形式暴露通量。使用这个配方，我们提出了一个系统，产生一个易于处理的最小二乘有限元公式，并建立理论来支持这种方法。最小二乘有限元逼近自然提供了后验误差估计器，并且我们提供了支持该方法的数值证据。计算结果突出了各种分子构型的自适应网格细化的情况下的最优性。特别是，我们表现出良好的性能的玻恩离子。束蛋白I甲醇和偶极子，这突出了我们方法的鲁棒性。(C)2009年，Wiley期刊。Inc. J Comput Chem 31：1625-1635，2010
The Poisson-Boltzmann equation is an important tool in modeling solvent in biomolecular systems. In this article. we focus on numerical approximations to the electrostatic potential expressed in the regularized linear Poisson-Boltzmann equation. We expose the flux directly through a first-order system form of the equation. Using this formulation, we propose a system that yields a tractable least-squares finite element formulation and establish theory to support this approach. The least-squares finite element approximation naturally provides an a posteriori error estimator and we present numerical evidence in support of the method. The computational results highlight optimality in the case of adaptive mesh refinement for a variety of molecular configurations. In particular, we show promising performance for the Born ion. Fasciculin I. methanol, and a dipole, which highlights robustness of our approach. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 31: 1625-1635, 2010